DNA fingerprinting has been widely applied to examine the genetic variation for the purpose of biological conservation. Microsatellites DNA with short sequence repeats provide high variability and high resolution in assessing population genetic structure. In this study, genetic diversity and population structure of Chamacyparis formosensis Matsumura were examined. In the past decades, human overexploitation has caused the population decline in the relic species. The microsatellite DNA diversity of C. formosensis is high within populations and species. Population of South-cross-island highway that processed the highest level of genetic diversity should be considered as a hot spot, as indicated by its demography. For maintaining the genetic diversity of C. formosensis, lowering down the disturbances that impact the habitats and increasing the effective population size are required. Microsatellite DNAs, which are able to distinguish individuals and populations, provide molecular ID for conservation.

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